I want to develop test code for 2 Arduino Due's hooked each up to a USB hub which is hooked up to an Apple Macbook. The Arduino code would just have one Due send a a couple bits to the other Due, which sends them back to the first, via input/output bits, to prove it works.

Is this possible? Or do you have to plug in one at a time to do development (compiling / downloading / debugging)? Or is there some other way to do it?

as far as I know if you have different arduino applications open whatever you set in one will be the setting in the other, though it may not show it

I ran into this not too long ago where I was developing on a mega, but the final target was a 328P device so I opened up another arduino IDE, loaded the arduinoisp sketch to the 328, went back to the mega window attempted to upload a change and got an invalid device signature error from the mega, which the signature was for the 238P.

So, if I needed the ability to run multiple Due's at once, where each of them could require breakpoints & debugging, then the only safe way would be to have a computer per Due? That is, 4 Due's would require 4 Airbooks (or PCs) in order to debug all 4 at once, with each Due having a one-to-one connection with its own host computer?

I've had 2 IDEs running with 2 serial ports open talking to the 2 serial ports on a '1284P.Don't know why 3 or 4 would be any different, say with a Mega and more USB/Serial adapters, or with more cards.